Alternative RNA splicing in stem cells and cancer stem cells: Importance of transcript-based expression analysis

Table 2 Alternative splicing analysis tools based on isoform-based method and count-based method (including the exon- and event-based approaches)

Tools	Human/ plants/ animals	Types of detecting splices	Type of tool	Year of publish	Ref.	Citation
Isoform-based method
Cuffdiff2	All	-	Linux	2012	[109]	9550
HMMSplicer	All	-	Linux	2010	[110]	79
PennDiff	All	-	Linux	2018	[111]	9
rSeqDiff	All	-	R	2013	[112]	29
DiffSplice	All	-	Windows/Linux	2013	[113]	141
NSMAP	All	-	MatLab package	2011	[114]	46
MISO	All	SE / A3SS / A5SS / MXE / TandemUTR / RI / AF / AL	Linux	2010	[115]	1166
Exon-based method
TopHaT	All	-	Linux	2009	[116]	11026
DEXSeq	All	-	R	2012	[117]	1091
edgeR	All	-	R	2010	[118]	19012
JunctionSeq	All	-	R	2016	[119]	81
limma	All	-	R	2015	[120]	11033
rSeqNP	All	-	R	2015	[121]	10
Event-based method
MAJIQ	All	SE / A5SS / A3SS	Linux	2016	[122]	171
rMATS	All	SE / A5SS / A3SS / RI / MXE	Linux	2014	[123]	746
SUPPA	All	SE / A5SS / A3SS / RI / MXE / AF / AL	Linux	2015	[124]	134
SUPPA2	All	SE / A5SS / A3SS / RI / MXE / AF / AL	Linux	2018	[125]	-
ASGAL	All	SE / A5SS / A3SS / RI	Linux	2018	[126]	12
Astalavista version 3.0	All	SE / A5SS / A3SS / RI	Linux	2012	[127]	62
LeafCutter	All	SE / A5SS / A3SS	Linux	2018	[128]	200
SpliceGrapher	All	SE / A5SS / A3SS / RI	Linux	2012	[129]	132
KisSplice	All	SNPs, indels and AS events (SE / A5SS / A3SS / RI )	Linux	2012	[130]	-
Alt Event Finder	All	SE	Linux	2012	[131]	24
Matt	All	SE / A5SS / A3SS / RI	Linux	2018	[132]	14
ALEXA-seq	All	SE / A5SS / A3SS / RI	Linux	2010	[133]	340
Outrigger	All	SE / A5SS / A3SS / RI	Linux	2016	[134]	86
ASDT	All	SE / A5SS / A3SS / RI	Perl	2018	[135]	5
SplicePie	All	SE / RI	R	2015	[136]	17
VAST-TOOLS	All	SE / A5SS / A3SS / RI	R	2017	[137]	118
spliceR	All	SE / A5SS / A3SS / RI / AF/AL	R	2014	[138]	80
Pro-Splicer	Human	SE / A5SS / A3SS	Website (http://prosplicer.mbc.nctu.edu.tw/)	2003	[139]	50
ASPicDB	Human	SE / A5SS / A3SS / RI / AF/AL	Website (http://srv00.recas.ba.infn.it/ASPicDB/)	2006	[140]	33
H-DBAS	Human	SE / A5SS / A3SS / RI / AF/AL	Website (http://www.h-invitational.jp/h-dbas/)	2007	[141]	56
ASIP	Plant	SE / A5SS / A3SS / RI	Website (http://www.plantgdb.org/ASIP/)	2006	[142]	535
ASG	Human	SE / A5SS / A3SS / RI	Website (https://brcwebportal.cos.ncsu.edu/asg/)	2004	[143]	116
VastDB	vertebrate	SE / A5SS / A3SS / RI	Website (https://vastdb.crg.eu/wiki/Main_Page)	2017	[137]	118
Astalavista	Human/ Animals	SE / A5SS / A3SS / RI	Website (http://astalavista.sammeth.net/)	2007	[144]	205
SpliceDitector	Plant/ Human	SE / A5SS / A3SS / RI	Windows	2018	[11]	1
dSpliceType	All	SE / A5SS / A3SS / RI / MXE	Windows/ Linux	2015	[145]	4
AltAnalyze	All	SE / A5SS / A3SS / RI / MXE	Windows/ Linux	2010	[146]	253

SE: Skipped exon; A3SS: Alternative acceptor site; A5SS: Alternative donor site; RI: Retained intron; MXE: Mutually exclusive exons; AF/AL: Alternative first/last exons.